Checkpoint of shell optimization

fix(cli): Write shell command output to a file and limit memory buffered in UI

Fixes.

Checkpoint.

fix(core, cli): await outputStream.end() to prevent race conditions

This commit fixes a critical race condition where
was called synchronously without being awaited. This led to potential file
truncation or EBUSY errors on Windows when attempting to manipulate the file
immediately after the  call.

Additionally, this change removes fixed wait times (`setTimeout`) that
were previously used in test files as a band-aid.

fix(core): stream processed xterm output to file to remove spurious escape codes

test(core): update shell regression tests to use file_data events

packages/core/src/tools/shell.test.ts

@@ -119,6 +119,7 @@ describe('ShellTool', () => {
       getDebugMode: vi.fn().mockReturnValue(false),
       getTargetDir: vi.fn().mockReturnValue(tempRootDir),
       getSummarizeToolOutputConfig: vi.fn().mockReturnValue(undefined),
+      getTruncateToolOutputThreshold: vi.fn().mockReturnValue(40000),
       getWorkspaceContext: vi
         .fn()
         .mockReturnValue(new WorkspaceContext(tempRootDir)),